Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

Abstract

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

“…Because UCEs are conserved across most vertebrate groups [20] and found in groups including yeast and insects [19], our framework is generalizable beyond this study and relevant to resolving ancient phylogenetic enigmas throughout the tree of life [28]. This approach to highthroughput phylogenomics-based on thousands of loci-is likely to fundamentally change the way that systematists gather and analyse data.…”

“…We also used each alignment to estimate gene trees incorporating 1000 multi-locus bootstrap replicates, which we integrated into STEAC and STAR [24] species trees. Additional details concerning UCE sequence capture methods and phylogenetic methods are available in Faircloth et al [20].…”

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

“…Recently developed methodologies such as restriction site‐associated DNA sequencing (RAD‐seq, Miller et al., 2007) and target capture using ultraconserved elements (UCEs, Faircloth et al., 2012) or anchored hybrid enrichment (AHE, Lemmon, Emme, & Lemmon, 2012) now allow researchers to obtain reduced representation genomic coverage across many individuals. All three types of data collection have been shown to be appropriate for phylogeographic‐level studies of vertebrates, including RAD‐seq (Manthey & Moyle, 2015), UCEs (Smith et al., 2013), and AHE (Brandley et al., 2015), suggesting these methods’ ability to resolve the evolutionary history of A. carolinensis .…”

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

“…The era of using genome-scale data to reconstruct the evolutionary history of organismal groups has recently begun (Alföldi et al 2011;Faircloth et al 2012;McCormack et al 2012;Jarvis et al 2014;Prum et al 2015). Due to the increasing numbers of whole-genome data sets that are publicly available, it is now straightforward to use in silico methods to discover and design hundreds or thousands of new loci such as "anonymous loci" (ALs) (Karl and Avise 1993;Peng et al 2009;Wenzel and Piertney 2015), exon-primed intron-crossing or "EPIC" loci (Palumbi and Baker 1994;Li et al 2010), conserved nuclear exon loci (Li et al 2007), anchored enrichment "AE" loci Lemmon and Lemmon 2013), and ultraconserved element "UCE" loci McCormack et al 2012) for use in phylogenomic studies.…”

“…Due to the increasing numbers of whole-genome data sets that are publicly available, it is now straightforward to use in silico methods to discover and design hundreds or thousands of new loci such as "anonymous loci" (ALs) (Karl and Avise 1993;Peng et al 2009;Wenzel and Piertney 2015), exon-primed intron-crossing or "EPIC" loci (Palumbi and Baker 1994;Li et al 2010), conserved nuclear exon loci (Li et al 2007), anchored enrichment "AE" loci Lemmon and Lemmon 2013), and ultraconserved element "UCE" loci McCormack et al 2012) for use in phylogenomic studies. Once loci are designed, NGS target-capture methods are employed to obtain orthologous sequences from many different individuals or species (e.g., Faircloth et al 2012;, which results in data sets with orders of magnitude more loci than in previous years.…”